diff options
| -rw-r--r-- | ml_exp/compound.py | 9 | ||||
| -rw-r--r-- | ml_exp/representations.py | 15 |
2 files changed, 10 insertions, 14 deletions
diff --git a/ml_exp/compound.py b/ml_exp/compound.py index 1598fa482..4dbd8c95c 100644 --- a/ml_exp/compound.py +++ b/ml_exp/compound.py @@ -116,18 +116,15 @@ class Compound: forces, size=size) - def gen_bos(self, - size=23, - stuff='bonds'): + def gen_bob(self, + size=23): """ Generate the Bag of Stuff for the compound. size: compound size. - stuff: elements of the bag, by default the known bag of bonds. """ self.bos = bag_of_stuff(self.cm, self.atoms, - size=size, - stuff=stuff) + size=size) def read_xyz(self, filename): diff --git a/ml_exp/representations.py b/ml_exp/representations.py index ea079595e..d4e79c7d9 100644 --- a/ml_exp/representations.py +++ b/ml_exp/representations.py @@ -308,10 +308,9 @@ def check_bond(bags, return False, None -def bag_of_stuff(cm, +def bag_of_bonds(cm, atoms, - size=23, - stuff='bonds'): + size=23): """ Creates the Bag of Bonds using the Coulomb Matrix. cm: coulomb matrix. @@ -366,19 +365,19 @@ generated as the vector of eigenvalues, try (re-)generating the CM.') bonds.append(''.join(sorted([a_i, a_j]))) bonds = atom_list + bonds - # Create the final vector for the bos. - bos = np.zeros(bond_size, dtype=float) + # Create the final vector for the bob. + bob = np.zeros(bond_size, dtype=float) c_i = 0 for i, bond in enumerate(bonds): checker = check_bond(bags, bond) if checker[0]: for j, num in enumerate(sorted(bags[checker[1]][1:])[::-1]): - # Use c_i as the index for bos if the zero padding should + # Use c_i as the index for bob if the zero padding should # be at the end of the vector instead of between each bond. - bos[i*size + j] = num + bob[i*size + j] = num c_i += 1 else: print(f'Error. Bond {bond} from bond list coudn\'t be found', 'in the bags list. This could be a case where the atom', 'is only present oncce in the molecule.') - return bos + return bob |